I get an intermittent engine warning light at 5000 rpm in third gear. It clears after shifting or lowering the rpm. No locked in faults using durametric.

 

is it the dashboard CEL? and is it only at 5k rpm, in 3rd? i.e. what if you hit 6k in 4th etc. i remember test driving an M3 once and i would get some kind of warning and gas would cut off at 5k. i was told by sales rep (whether this is BS, i have no idea) that they set the ECU that way to avoid test drivers joy riding. boy did they know ME well.

but i was thinking that if it's happening in all gears at exactly 5k rpm, it sounds like some kind of limiter.

 

To follow up on what Jiffy said, you may have inadvertently set speed warning in nanny section of pcm. I did this once. May not be rpm which is issue but speed warning. Try going in and removing it.